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In a section of space, a white hole has opened and is consuming the surrounding space and planets. It has reached the planet, Sultath, where Jack Harkness and Tara Mishra are. Jack is trying to get the two of them off the planet, but interference from the hole prevents the vortex manipulator from working. He tries to contact the Ninth Doctor, but the interference affects the communication, and the Doctor assumes Jack is in a bar somewhere. With the Doctor not coming to their rescue, it seems all is lost, until the arrival of a mysterious woman in Gallifreyan armor.

At St Luke's University, the phone in the Doctor's chambers starts ringing. Nardole answers the phone, and tells the person calling to hold, while he takes the phone and runs off down the hallway.

Over in the library, the Twelfth Doctor is looking at history books and tossing aside ones that are inaccurate, an act that makes it difficult for Bill Potts to study. Nardole arrives, handing the phone to the Doctor. The person on the other end tells him that she's dropping in for tea. The Doctor walks over to the nearby window and sees something that makes him turn around and yell for everyone to get out.

A bowship crashes into the library. The trio are perfectly unharmed, with Nardole protecting Bill. The Doctor remarks on the ship, before the cockpit opens, revealing the armored woman from earlier. However, the helmet is now off, revealing that she is Jenny, the Doctor's daughter.

Meanwhile, the Tenth Doctor, Gabby Gonzalez, and Cindy Wu are traveling in the Doctor's TARDIS. The Doctor is telling the two women about an adventure he had, when the Cloister Bell starts ringing. Suddenly, the trio find themselves in an earlier version of the TARDIS, and the Third Doctor is on the floor, being consumed by some white energy. The Tenth Doctor tries to help him, but the Third Doctor and his TARDIS fade away, leaving the trio back in their own TARDIS. According to the Tenth Doctor, the two TARDISes were merging, so his TARDIS had used an emergency temporal displacement to escape.

Back at the university, the four have moved to the Doctor's chambers and are enjoying some tea. Nardole is concerned. The Doctor assumes it's about the Vault, but he checked it, and it's completely fine. Nardole corrects him by saying he's more concerned about the crashed bowship, but the Doctor has dealt with that by calling in UNIT.

At the crash site, Kate Stewart has had the area closed off. Petronella Osgood marvels at the ship. But, as she touches it, her hand gets shocked by the strange white energy.

Back with the quartet, Jenny explains why she came here. After meeting Jack and Tara, Jenny tried to save them, but the white hole consumed the duo. Jenny rushed back to her ship and followed them in, hoping to save them. But, the ship couldn't handle the stress and it looked like Jenny was doomed. However, luck was on her side, as the Fifth Doctor came to rescue her. After failing to extend the TARDIS's gravity shield around the bowship, the Doctor was left with no choice but to ram Jenny's ship. The bowship was freed, but the TARDIS was caught in the gravity of the white hole and was consumed.

Meanwhile, the Eleventh Doctor finishes repairing the TARDIS's translation matrix, allowing Alice Obiefune to be able to understand what he's saying. An alarm starts going off, prompting the Doctor to go check the console. The Doctor reveals that he lied when he told Alice that hearing the Cloister Bell was the worst thing that could ever happen. The alarm is being caused by the TARDIS's Doomsday Circuit, which goes off when it detects the end of time, or, in this case, space. The TARDIS flies into the white void.

Back at the university, the Twelfth Doctor asks how Jenny found him. She tells him that this is the only place and time he has stayed still long enough for her to locate him, that she was able to access. Bill has heard enough and knows they need to do something to help the Fifth Doctor, Jack, and Tara. Running over to the TARDIS, she reaches out her hand to open the door. As she touches the door, she is attacked by the white energy, which enters her body. At that moment, Kate and Osgood arrive. The Doctor asks Osgood to help him analyze the white energy attacking Bill, but she refuses. Osgood, Kate, and the UNIT soldiers have been possessed by the white energy. Osgood states that Bill will soon know peace, and so will the others.

On the Pacific Ocean, in 1886, a boat hits something in the water. Using a net, the men pull the object aboard, revealing it to be the TARDIS. The door opens and Rose Tyler steps out, wanting to know where she is. Not long after, the Ninth Doctor emerges. He gets into an argument with one of the sailors, only for it to be broken up by the captain of the ship, Madame Vastra, who welcomes the duo aboard the Mary Anning.

Inside her quarters, Vastra and Jenny Flint serve tea to their guests. Vasta and Flint explain to Rose about Vastra's origins. The Doctor asks Vastra why she's here. Vastra explains about how a Silurian corpse, one from the scholar class, was found and she is now looking for other possible Silurian survivors. The Doctor quickly dismisses the idea and starts to depart with Rose. But, Rose mentions that the Doctor's taking her to meet a guru who has three eyes. Vastra knows the Doctor is hiding something and confronts him, but before she can get any answers, the ship is hit by a creature who wrecks the boat.

The next morning, Rose awakens to find herself, the Doctor, Vastra, Flint, and a couple of sailors alive on an island. Vastra identifies the creature as a Myrka. She's angry at the Doctor for keeping his secrets, as they have now cost her the ship and half her crew. At that moment, the group is surrounded by Silurians. Vastra starts to greet them, but one of them shoots her. The Silurians take everyone except Flint away, while she stays behind to tend to the unconscious Vastra.

The group is led to the leaders of the tribe. The Doctor greets one of them, Horlak, who recognises the Doctor. Horlak asks the Doctor why he has come here. The Doctor brings Rose forward. After the incident with Addison Delamar, Rose's mind was left fractured. According to the TARDIS, Rose is on the verge of a full psychotic episode. Horlak reaches into Rose's mind and begins healing it. A voice calls out from within Rose's mind, one Rose recognises to be Jack Harkness.

Jack has established a psychic projection through Horlak, so he can communicate with the Doctor and Rose. The Doctor asks Jack how he pulled this off, and Jack steps aside to allow someone else to speak. To the Doctor's surprise, the person responsible is the Fourth Doctor. The Fourth Doctor explains that the universe is being devoured. But, the projection begins to break down. The Ninth Doctor uses his sonic screwdriver to boost the signal, but gets interrupted by the arrival of Vastra and Flint, resulting in the projection fading away.

The Doctor is furious with Vastra, but Vastra is just as angry. She demands for the Doctor to tell her why he hid this tribe from her. As it turns out, this tribe of Silurians have a disease, Raldoma Syndrome. It doesn't affect the scholar Silurians, but it does affect the warrior Silurians, like Vastra. Years ago, the Sixth Doctor helped set up this place, a location to keep these Silurians under quarantine, so they can't infect any other Silurians.

Rose calls out to the Doctor, pointing out that some of the Silurians have been infected by the white energy. Even Vastra and Flint get infected. Rose quickly picks up one of the Silurian guns and shoots Vastra, freeing her from the energy. The Doctor takes the gun and adjusts it with his screwdriver, allowing him to use it to free everyone else in the room from the corruption.

After freeing everyone, the Doctor asks Horlak if he can borrow another gun, as his modification ruined the first gun. Horlak agrees and states that he and the others will creating a telepathic dam to block the corruption of the white energy. As everyone begins to leave, Horlak calls the Doctor back, in order to give him another message from his past.

Later, the Doctor joins everyone else back at the TARDIS. The Doctor moves the TARDIS to 13 Paternoster Row. He then asks Vastra to look after Rose, as he's going somewhere dangerous that might be the end of him. The Doctor departs in the TARDIS. Flint assures Rose that the Doctor knows what he is doing, most of the time. Unknown to the two of them, Vastra and the sailors have been possessed by the white energy.

In his TARDIS, the Tenth Doctor stares at a projection of the Third Doctor being attacked by the white energy, while Cindy is wondering just how old the Doctor really is. Suddenly, the TARDIS shakes. The Doctor checks the console and sees they've encountered a temporal funnel and extreme gravitational stresses that are pulling the TARDIS off course.

The TARDIS ends up near a space station poised on the brink of the gravity well of a cluster of neutron stars. It's also linked to another region of space via a hyperspace corridor. The Doctor makes an emergency landing aboard the station, while wondering what kind of force could draw the TARDIS off course.

The trio step outside, and the Doctor realises that the station is a power refining facility, mining energy from the neutron helix. An alarm tells them that the station, Poseidon, is on lockdown. At that moment, two officers, Co-ordinator Akiyama and Senior Hyperspace Tech Mouchgober enter the room. They call out to the Doctor, apparently recognising him. However, it turns out they are mistaking him for Doctor Bell, who is supposed to be visiting the station to conduct an inspection. The Doctor and Gabby quickly trick them into believing that Bell is detained and that the trio are a replacement team.

The two officers bring the trio to Central Control, where Director Jessop is not happy to see them. The trio have come at a bad time, as the neutron helix, known as Hades' Helix, is flaring up. The helix is producing a large amount of electromagnetic radiation. The Doctor quickly moves over to a nearby console. With some adjustments, the Doctor not only fixes the shields, but improves them. With the immediate crisis resolved, Jessop asks Akiyama to take Cindy on an inspection tour, while he will show the Doctor and Gabby around Central Control.

Jessop explains that the station is the core collection point for the energy mining. They use collection probes to mine the energy. The probes beam the energy to the station, which transmits the energy through the corridor to the power collection plant at Ultima Tarsus. The corridor also serves as the anchor for the station, protecting it from the helix's gravitational forces.

Meanwhile, Akiyama and Cindy are down at the docking ports. Akiyama points out one of the collection probes, floating in space. She mentions that two probes when missing some time ago. Cindy notices that the probe is moving to dock with the station, something that the probes are not supposed to do. Cindy suggests it might be one of the missing probes. To Akiyama's shock, it is one of the lost probes.

Back in Central Control, Jessop tells the Doctor about the missing probes. One of the officers calls the group over to his console. According to the readings, the helix is collapsing inward at an impossible rate, becoming a black hole. The Doctor states it's not impossible, but is widely accelerated, possibly artificially. At that moment, Gabby gets a text from Cindy, about the missing probes docking with the station. The Doctor patches Cindy into the comm unit and tells her to get away from the docking port. Whoever is inside the probe is not friendly.

The station shakes as it's bombarded by time distortions. According to the Doctor, this is not a natural phenomenon, but one that's been engineered. Looking at a nearby screen, the Doctor and Gabby see the distortions are being caused by the white energy they saw attack the Third Doctor. The scanners then detect approaching ships, that turn out to be Cyberships. The Doctor yells at Cindy to run away from the docking port, as the station is being invaded by the Cybermen. At that moment, the docking hatch opens, and Cybermen start swarming into the station, attacking the security officers, while Akiyama and Cindy run.

Back at Central Control, the Doctor watches the Cybermen infect the security officers, with what looks like some new Cyber-virus. Mouchgober reports that the second probe is docking, which means there will be more of them, but Jessop has changed the access cipher, which will slow them down. But, as the Doctor points out, not for long, for the Cyberships arrive, and Cybermen starting flying through space, towards the station. The Doctor tells Jessop that he needs to evacuate the station, as this could be the only chance to get everyone to safety, especially with the helix collapsing into a black hole.

While Jessop gives the evacuation order, the Doctor talks to Gabby. The Cybermen were already here, planning the attack. But, the helix's sudden mutation means something else is going on here. Right now, they need to plot a safe route for Cindy and Akiyama to get back to Central Control. While Gabby does this, the Doctor overhears Jessop talking to another officer. The civilian personnel have been safely launched from the station and into the corridor. However, the Cybermen have trashed the lower docking ring. There are no escape ships left for the officers to use.

The station shakes, as the Cyberships ram into it. This baffles the Doctor, as the Cybermen aren't acting logically. Then it hits him. There is no Cyber-virus. It's the white energy, which has infected the Cybermen. The Doctor does a deep scan of the collapsing helix, and finds that it's not becoming a black hole, but a white hole. Streams of time distortions are emanating from the hole, reaching out for the station, even accounting for the station's continual drift. There is an intelligence within the hole.

The Doctor tells Jessop that he and his crew need to evacuate now. Since there are no escape ships, the crew will have to use the collection probes. The Doctor will use the station's power beam to push the probes through the corridor, allowing them to safely arrive at Ultima Tarsus. They should also destroy the station, so that the Cybermen can't use the corridor. The Cybermen were planning on taking over the station to use as a platform to stage an invasion of Ultima Tarsus. However, their plan was ruined by the white energy. Jessop and his crew need to make it back to Ultima Tarsus, to inform people about what happened here, so something like this can't happen again. Jessop agrees and begins working on the evacuation, and priming the station to self destruct.

Gabby then reports a problem. The increasing number of Cybermen is limiting the options she can use to safely guide Cindy. The Doctor points out that they can go through the vacuum core. But, the core is where the energy beam is generated and there's no air in there. Cindy hears this and tells the Doctor that she hates him. The Doctor ignores this and tells Cindy to go through the core.

Outside the core, Akiyama gives Cindy a cube, containing a self-enclosing E-Suit. All she has to do is tap the cube to her chest and the suit will form around her. As Akiyama begins explaining what will happen when they open the access hatch, Cindy puts on her suit. She then notices the Cybermen behind Akiyama and tries to warn her. But, it's too late, as a Cyberman grabs Akiyama, infecting her. Her suit cube files out of her hand and into Cindy's. The Doctor tells Cindy to not let the Cybermen touch her. She tosses the cube at the Cybermen, causing the lead one to stumble and slow down the others. However, the infected Akiyama grabs Cindy's ankle, just before Cindy opens the access hatch, and everyone is blown into the core.

The Doctor orders Gabby to go get Cindy and to take her back to the TARDIS, without removing Cindy's suit. The Doctor heads over to Jessop and his crew, who have boarded a collection pod. Jessop thanks the Doctor for his help, before launching the pod. The Doctor then re-aligns the energy beam, pushing the pod safely through the corridor.

The Doctor runs back to the TARDIS, noticing that the white hole has begun consuming the local space. At the TARDIS, he meets Gabby and Cindy. To his surprise, Cindy isn't infected. With no time to ponder on this, the trio quickly get inside the TARDIS and dematerialise, seconds before the station self destructs. The TARDIS is unable to get away, however, as one of the white hole's tendrils grabs onto the ship. As the Doctor ponders over everything, someone or something starts knocking on the door, which the Doctor proclaims to be impossible.

Inside the white void, the Eleventh Doctor confirms that there's nothing outside the TARDIS. Alice comments on it, giving the Doctor an idea. Even nothing has to have some substance, a point of origin. Scanning again, the Doctor detects a pinhole anomaly, so small that it's almost undetectable. The Doctor decides to fly the TARDIS through the anomaly, but that requires for him to shrink the TARDIS's external dimensions to do so. Despite Alice's protests, the Doctor goes through with it.

On the other side, the TARDIS returns to normal size as it lands on a planet. Checking the console, the Doctor is shocked to discover where they landed. They are on Gallifrey, in the ancient past. Alice suggests that they should leave, but the Doctor reveals that the fluid links were destroyed. They need mercury to repair the TARDIS, and they can only get some from outside. Since they are on Gallifrey, the Doctor must not interfere with events, so the two will have to lay low.

To prevent the TARDIS from being discovered, the Doctor sets up a dampening field and moves the ship to a house the two rent. Since he can't get the mercury, the Doctor spends his days checking over the other systems on the TARDIS, noting that the TARDIS is strangely exhausted from its trip through the micro-conduit.

One day, the Doctor decides to check out a trading post in the Higher City, that dealt with secondhand scientific equipment, with the hope it might have something he can use. As they pass near the TARDIS shipyard, they find themselves in a time loop, but not a powerful one, as the Doctor is able to shield both himself and Alice from the effects with his sonic screwdriver. The two investigate to discover a group of scientists attempting to use a D-Bubble Fluxer to imprint one of the first TARDISes with larger interior dimensions. However, the time capsule has gone out of control, and is attacking and consuming the scientists.

Using his screwdriver, the Doctor has the time capsule focus on him. He speaks to it, calming it down, and resulting in it releasing the scientists it has captured. He gives the scientists some advice and asks for some spare fluid links. The scientists ask who he and Alice are, so he introduces them as "Alice and the other one". The Doctor and Alice try to come up with a name for him to use, before the Doctor decides to have everyone call him "Theta-Sigma". Watching all this from a balcony is Rassilon, who orders Prefect Sarkis to bring Theta-Sigma to him.

In his office, Rassilon studies the Doctor's screwdriver, noting how sophisticated it is. He also has the distinct feeling he has met the Doctor before. The Doctor denies this, stating that he is a humble inventor from the cheese-making quarter of the Lower City. Rassilon isn't fooled. The Doctor is clearly a Level 7 Evolved Time Sensitive, just like Rassilon is. Rassilon asks the Doctor how he was missed by the census. The Doctor reveals it was because he put down making cheese as his primary skill, telling him to ask Alice to confirm this. This leads to Rassilon mistaking Alice to be the Doctor's wife.

Rassilon asks the Doctor why he asked the scientists for fluid links. The Doctor makes a comment that the current use of Validium in the links is dangerous, and that they should use Mercury or Rubidium instead. Rassilon is impressed with the Doctor's knowledge and decides to have him become one of the test pilots.

As the days go by, the Doctor helps the Gallifreyans develop the time capsules in ways that were unobtrusive or would have little impact on future developments. One day, a test flight is scheduled to occur. Three time capsules will be jumping days forwards and backwards in time. The Doctor has been selected as one of the pilots. He plans to move the time capsule to where the TARDIS is, and then use the capsule's fluid links to repair the TARDIS, allowing the duo to depart.

Alice heads back to the TARDIS to wait for the Doctor. When she gets there, she finds a floating hypercube inside. The cube greets her, projecting the image of the Second Doctor. The Doctor tells Alice to warn his future incarnation to avoid piloting the Type 1 TARDIS at all costs.

As Alice runs to the test chamber, the Eleventh Doctor is already there. He notes that the capsule assigned to him is the same one he calmed down before. Rassilon had done this on purpose, as he figured that the flight would go more smoothly, since the Doctor has a sort of bond with the capsule.

The test commences and the first two TARDISes dematerialise successfully. However, when the Doctor tries to dematerialise his capsule, something goes wrong. Rassilon tells him to abort the flight, but it's too late, as the TARDIS vanishes after entering the Time Vortex.

One of the scientists has determined that there was an extra dimensional bubble hidden in the capsule, likely left over from the first attempt to insert internal dimensions inside the plasmic shell. This second bubble was unstable. The moment the capsule entered the vortex, the bubble burst, causing a catastrophic dimensional breakdown.

Alice runs into the room, asking where the Doctor is. Rassilon breaks the news to her. The Doctor is lost, forever. Alice collapses to the ground and cries.

River Song and Wildar are on a mysterious planetoid. River has a mining drone following her. River asks for 'charges', which Wildar is immediately confused about, but soon, the ground behind River explodes. She jumps around, throwing more charges down, exploding more of the ground and tossing Wildar around, eventually reaching the 'Dacha'. River exclaims this, pleasured. Wildar, who had just fallen down into the pit River had just blown up, worries over his helmet being broken, though he slows as an army comes rushing towards him. A woman, Terra, after grabbing, and taking Wildar, makes him realize that they are speaking Silurian. Meanwhile, River Song is examining the Dacha. She calls for Wildar, with no response. Puzzled, she assumes the cave is too deep, and is blocking the signal. River climbs up to a vantage point, only to find various portraits of the Third Doctor, Ninth Doctor, Eleventh Doctor, and Twelfth Doctor, along with two TARDISes. River orders the mining drone to find Wildar, while she goes to find more of the Dacha. Meanwhile, Wildar is translating the Silurian to himself, as they discuss Wildar being a corrupt human. Wildar is incredibly nervous. Soon, in front of him, he sees a Silurian. He is perplexed by his existence. Meanwhile, the drone is still flying to the dig site, when bits of an 'exploding asteroid' pass the drone. River states confidently that it's an 'exploding asteroid that will endanger the planetoid'. River spots a pot in the center of the room, which she assumes is the Dacha, when a voice rejects this, and confirms that they are the Dacha. The voice turns out to be from another Silurian. River swiftly points her gun at the Silurian. The Silurian asks for help, in exchange for sparing Wildar, but River denies, claiming that she's not a 'saves everyone' type. Warriors ambush River, encircling her. Meanwhile, Wildar is in a pit, with a large dinosaur. Many people watch, cheering. River jumps down to help Wildar, and she finds out that Wildar has no charges left, and he didn't bring "the cutting laser". River starts to run, claiming that "she hates it when it's easy".

While preparing for an evening out in Paris, the Fourth Doctor and Romana discover a rift in the multiverse and materialize on a Kroton ship, and the Doctor is immediately puzzled at the Krotons' relative level of power compared to his past experience with them. His confusion increases when the Krotons are attacked by Quarks, followed by another attack from the United Confederation of Ogrons. Having retreated to the TARDIS, the Doctor broadcasts a message to all three attacking fleets, confirming that they originate from alternate universes, speculating that these fleets originate from worlds where the Daleks do not exist as the Daleks would have otherwise destroyed these three races to prevent them achieving this power. When the other fleets ask why the Daleks do not rule this universe if they are so powerful, the Doctor explains that this is because of him defeating them, and Romana then adds that the Doctor is actually the least dangerous of all Time Lords. Faced with this revelation, the fleets retreat back into the rift, but the Doctor takes the TARDIS in after them to find out what caused this attack in the first place.

Faced with the 'possessed' Kate, Osgood, and UNIT forces, the Doctor realises that the energy possessing them does not affect time-travelers, prompting him to order his companions to retreat to the TARDIS to figure out their next move. Once inside the ship, he realizes that they have arrived in the TARDIS of the Tenth Doctor, who is joyfully reunited with Jenny before she identifies the Twelfth Doctor as his future self. As Gabby and Cindy explain regeneration to Bill, the two Doctors deduce that the white energy infecting the world is the energy of anti-time, which was brought here by Jenny's bowship. Deciding to analyse the bowship directly, the Doctors and Jenny evacuate the TARDIS in an escape pod, but are confronted by a mass of possessed students before those students are knocked out by the Ninth Doctor. The Ninth Doctor begins to explain that he was instructed to come here by their fourth incarnation, but his explanation is interrupted when the anti-time energy concentrates into a massive rift in the sky above the three Doctors.

After leaving Messaline, Jenny's ship runs out of power, but she is eventually able to reconfigure her ship's shields into a hyperdrive generator. After jumping through space, she arrives on a planet orbited by a mysterious moon that appears every six months for a short time before it disappears again. After conducting work on the planet for six months, Jenny is able to get to the moon once it returns, where she finds and retrieves a bowship before discovering a rift in time.

Refusing to believe that the Eleventh Doctor has died, Alice waits until nightfall, before sneaking into the lab and stealing one of the two remaining Type 1 Time Capsules, setting off to try to find the Doctor.

As the Doctors face the rift above the university, the Twelfth Doctor suggests that he, the Ninth and Tenth Doctors use their TARDISes to move Earth slightly to take it out of range of the rift. Unable to implement this plan immediately as their TARDISes have merged into one ship, the Tenth Doctor and Jenny head further into the ship to find a means of separating their ships while the others try to stabilize the rift, only to run into the Eighth Doctor and Josie Day coming out of another rift. After the Eighth Doctor explains that the other Doctors have become trapped on the other side of the rift, the Ninth, Tenth and Twelfth Doctors depart in Jenny's bowship while the Eighth Doctor remains with the companions on Earth to try and contain the situation. Travelling through the rift, the three Doctors briefly make contact with their other eight selves in the rift before identifying the source of the anomaly as the Eleventh Doctor, merged with the Type One TARDIS. Entering the TARDIS, the Doctors learn that their other self has become trapped outside reality after the proto-TARDIS panicked, but when he linked himself to the TARDIS's telepathic circuits to try and convince it to return to the universe, the TARDIS instead chose to try and destroy the universe due to its perception of the universe's chaotic state. In order to convince the Type One TARDIS to stop, the Doctors link their TARDISes to the other ship, the TARDIS's own perception of the universe helping its predecessor recognise that its initial perception was wrong. With the rift ended, the Doctors return to the university, the Ninth and Tenth Doctors agreeing to help the Eighth and Eleventh Doctors return to their TARDISes after they repair Jenny's ship, while the memories of all non-Time Lords of these events begin to fade so that even Bill and Nardole do not remember what has just happened.

This is Jenny's first appearance outside of flashbacks and cameos since her introduction in The Doctor's Daughter.

The first issue features Nardole's debut in comics.

Jenny is elated to make contact with the Fifth Doctor and exclaims "Dad!" when she hears his voice. This is a nod to the fact that, in the real world, Fifth Doctor actor Peter Davison is the father of Georgia Moffett, who portrayed Jenny in the series.

The Ninth Doctor Special addresses the differences between the Silurians seen across the TV series, featuring all three variants. Vastra, of the subspecies first seen in The Hungry Earth, is identified by Silurian guards, identical to the original Silurians from Doctor Who and the Silurians, as a "Warrior". She in turn identifies the corpse of such a Silurian as being of the "Scholar caste". This tribe is led by Horlak who is flanked by Silurians of the kind seen in Warriors of the Deep. The appearance of Horlak himself is derived from an unused "three eyed" design which was sculpted for The Hungry Earth.

Appearing separately in River Song's story is the Dacha, a Silurian male resembling Vastra's subspecies but with a third eye.

The Ninth Doctor converses with the Fourth Doctor via psychic projection, and later meets up with the Tenth and Twelfth Doctors. This marks the first time in the Doctor Who franchise where the Ninth Doctor is shown interacting with one of his other incarnations outside of a meeting involving every Doctor. The closest previous occurrence of this would be in the audio story Night of the Whisper, in which the Eleventh Doctor leaves a video message for the Ninth Doctor, who recognises his successor, but the two do not truly meet. The tie-in website whoisdoctorwho.co.uk also implies that the Seventh and Ninth Doctors once met, but it is left ambiguous, and the comic story Four Doctors shows his three successors looking over him, but he is unaware of their presence.

Despite Special #1 being marketed as three separate stories with River Song, the Fourth Doctor, and Jenny; only stories for the first two were in the issue. Likewise, Special #2 was marketed the same, but contained the conclusion to River's story, a story for Jenny between The Doctor's Daughter and the Alpha issue, and a story for Alice Obiefune immediately after issue four.

Talking with the Twelfth Doctor, the Tenth Doctor notes that he has a feeling he's going to like being the Twelfth. This is an improvement from the last time they met, where they were decidedly less civil. (COMIC: Four Doctors) He also gets along well with the Ninth Doctor, whom he'd previously suggested he disliked due to being "born in battle". (TV: Journey's End)

For the second time, the Tenth Doctor, upon meeting the Twelfth Doctor, assumes he is his immediate successor. The first was in the comic story Vortex Butterflies.

Issue six shows us that sections of the Ninth and Tenth Doctor's TARDIS console room walls slide up to reveal doors, being one of the few stories to show how this console room connects to the rest of the TARDIS. Previously, a wide circular door opening to a spiral staircase that leads to the TARDIS laundromat is seen in the comic story Laundro-Room of Doom.

River finds depictions of the Doctor's third, ninth, eleventh, and twelfth incarnations in the Silurians' cave, and is later shown visions of the latter three; it's unclear if this story takes place before or after The Husbands of River Song as she's unaware of the Twelfth Doctor's existence until then. She is referred to as a professor, setting it after her release from Stormcage.

Despite Jenny's story in part seven beginning at the ending of the television story The Doctor's Daughter, Jenny is wearing a white t-shirt and not the army green t-shirt seen in the episode.

The color of the Ninth Doctor's jumper changes from grey/black from The Ninth Doctor Special, to mauve in The Twelfth Doctor Special, to slate green in Omega, despite there being no narrative gaps between the latter two.

For Vastra and Flint, this story is set before they met Strax and as such is their first appearance without him.

When the Doctor is explaining the early TARDISes, Alice says, 'I see'. to which the Doctor replies, 'no you don't but it's kind of you to try'. He previously had a similar interaction with Laurence Scarman in TV: Pyramids of Mars.

The Tenth Doctor refers to the Ninth as "me with the ears" (TV: Rose) and the Twelfth as both "me with the eyebrows" (TV: Deep Breath) and "Granddad", a nickname bestowed upon the War Doctor by the Eleventh. (TV: The Time of the Doctor)